flye log

[MostafaYA]

flye log

[incoherentian]

I bet he could change that, but then...

SOME TIME LATER...

⠀⠀⠀⠀⣴⠶⠶⠶⠶⠶⠞⠛⠛⠛⠶⠶⠶⠒⠛⠛⠒⠶⠶⠶⠒⠒⠒⠒⠶⠶⠖⠚⠓⠶⢦⣤⣤⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⣿⠀⠀⢀⣀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⢀⠀⠀⠀⣹⡆⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⢸⡇⠀⣿⣿⡇⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⣿⠇⠀⢠⡟⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⣸⡇⠀⠈⠋⠁⠀⠀⠀⠈⢙⠷⠦⣄⣀⠀⠀⠀⢀⠀⠀⠀⠀⠀⠀⣀⣠⣤⣤⡀⠀⠀⠀⠀⠀⢸⡅⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⢻⡇⠀⠀⡀⠀⠀⠀⢀⠞⠁⠀⠀⠀⠈⠙⠲⢤⣸⣄⣤⠴⠖⠛⠉⠉⠁⠉⢢⠀⠀⠀⠀⠀⠀⢸⡇⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠈⣷⠀⠀⠃⠀⠀⠀⡎⠀⠀⠀⡴⠋⡉⠲⡀⠀⢻⡏⠀⠠⠒⠐⠲⡄⠀⠀⠀⢇⠀⠀⠀⠀⢠⡿⠀⠀⠀⠀⠀⢀⣀⣤⠤⢤⡀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⣿⠀⠀⠀⠀⠀⠀⡇⠀⠀⠀⡀⠸⣿⠂⡇⠀⣸⣇⠀⡇⠸⣿⠇⢸⠀⠀⠀⡜⠀⠀⠀⠀⢸⡇⢀⣀⣀⡤⠞⢋⣡⡤⣄⠈⢧⠀⠀⠀⠀
⠀⠀⠀⠀⠀⣿⡀⠀⠀⠀⠀⠀⠘⣄⠀⠀⠙⠲⠶⠊⠀⡔⠉⠉⢳⡘⠢⠤⠔⠁⠀⠀⣰⠃⠀⠀⠀⠀⢀⡟⠉⠉⢳⣤⠾⠋⠁⠀⠸⡆⠘⡆⠀⠀⠀
⠀⠀⠀⠀⠀⢸⡇⠀⠠⠀⠀⠀⢀⡈⠳⢤⣀⣀⣀⠤⠒⡇⠀⠀⢠⠧⣄⣀⣀⣀⡠⠞⠁⠀⠀⠀⠀⠀⣼⠃⠀⠀⠈⡿⠀⠀⠀⠀⣀⡇⠀⢧⣀⡀⠀
⠀⠀⠀⠀⠀⢸⡇⠀⠀⠀⠈⠀⠀⠉⠓⢒⣂⠀⠀⠀⠀⠀⠀⠀⠁⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⢸⡇⢀⣠⣴⠞⠃⠀⠀⠀⢸⠁⡀⠀⠀⠀⢹⡆
⠀⠀⠀⠀⣠⡼⢧⠀⠀⠀⠀⢀⠄⠊⣹⣿⣿⣿⠋⣷⣦⡀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠸⣿⠉⠁⠀⠀⠀⠀⠀⠀⢸⡟⠑⠀⠄⢰⣸⠇
⠀⢀⡴⠟⠁⠀⠈⡀⠀⠀⠀⠁⠀⠀⠉⠛⠿⠃⢰⣿⣿⣿⢢⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⣠⣤⡄⠀⢀⣿⠀⠀⠀⠀⠀⠀⠀⠀⠀⠛⠶⠾⠶⠋⠀⠀
⢠⡟⠀⠀⠀⠀⠰⡇⠀⣦⠀⠀⠀⠀⠀⠤⠤⢄⡀⠉⠉⠁⠀⢇⠀⠀⠀⠀⠀⠀⠀⠀⠀⣿⡿⠃⠀⣸⡏⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠈⢷⡼⠉⡦⠀⢠⣿⠀⢉⣤⣀⠄⣀⠀⠀⠀⠀⠉⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⡀⠀⠀⣿⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⢀⡾⠁⡼⠤⠤⠋⢸⣤⡜⠁⠀⠀⠈⢇⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠰⠟⠀⠀⣼⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⣼⠁⣸⣀⡤⠔⠊⢉⣠⣄⣀⠀⢀⡸⡾⢏⡉⠉⠓⢒⢶⠶⠶⠶⣶⡒⠲⠶⠦⢤⠤⠒⠒⠶⢤⣤⣤⡟⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⣇⣀⣠⣤⠴⠖⠚⢹⣇⣙⣒⣒⡧⠔⠀⠀⠈⠁⠒⠁⠈⢢⠀⡔⠀⠑⠤⠔⠊⠁⠀⠀⠀⠀⠀⠀⣿⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⠀⠀⠀⣿⠀⣤⣤⣤⣤⣤⠈⢩⣭⣭⣭⣭⠏⠀⠘⣭⣭⣭⣭⡉⢉⣭⣭⣭⣭⣭⠉⣿⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⠀⠀⠀⣿⠀⠉⠉⠉⠉⠁⠀⠈⠉⠉⠉⠉⢄⠀⢀⠊⠉⠉⠉⠀⢀⠽⢛⡙⠟⠛⢉⠉⢹⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⠀⠀⠀⢹⣶⣤⡤⠤⠤⣤⣤⣤⣤⣤⣤⣤⣤⣷⣧⣤⣤⣤⣀⠀⠁⠀⢸⣀⢴⣶⡿⠠⡾⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⠀⠀⠀⠀⢠⣏⠀⠀⠀⢀⡿⠀⠀⠀⠀⠀⠀⠈⠉⠉⠉⠙⠲⣤⣀⣀⠀⣁⣼⣿⣃⣾⠃⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⢹⠉⢻⠟⣿⣷⣶⣄⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠉⠉⠉⠉⡼⠃⣼⣿⣿⣿⣧⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⣾⠀⣿⡖⢋⣽⣿⣏⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⢀⣾⣷⣾⣿⡿⠋⠀⡸⠁⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠹⣀⣹⠟⢋⣽⢻⣿⡇⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠸⣿⣿⠿⣿⡥⠴⠚⠁⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠈⠿⠿⠛⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠻⠤⠤⠞⠁⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀⠀
"Dear Robert! It would be nice not to remove the porechop progress information..."  

😜

[incoherentian]

Hi Mostafa,

It is a pretty small section of the dragonflye log buried among kmc, trimming polishing etc. Is it possible you missed it?

The log of the initial flye execution starts with [dragonflye] Running: flye & the relevant lines are prepended with [flye],

e.g.

[dragonflye] Running: flye --nano-raw READS.fq.gz -g 4792047 -i 0 --threads 12 -o flye  2>&1 | sed 's/^/[flye] /' | tee -a dragonflye.log
[flye] [2023-10-05 14:11:46] INFO: Starting Flye 2.9.2-b1786
[flye] [2023-10-05 14:11:46] INFO: >>>STAGE: configure
[flye] [2023-10-05 14:11:46] INFO: Configuring run
[flye] [2023-10-05 14:11:49] INFO: Total read length: 203898539
[flye] [2023-10-05 14:11:49] INFO: Input genome size: 4792047
[flye] [2023-10-05 14:11:49] INFO: Estimated coverage: 42
[flye] [2023-10-05 14:11:49] INFO: Reads N50/N90: 19281 / 5303
[flye] [2023-10-05 14:11:49] INFO: Minimum overlap set to 5000
[flye] [2023-10-05 14:11:49] INFO: >>>STAGE: assembly
[flye] [2023-10-05 14:11:49] INFO: Assembling disjointigs
[flye] [2023-10-05 14:11:49] INFO: Reading sequences
[flye] [2023-10-05 14:11:57] INFO: Counting k-mers:
[flye] 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[flye] [2023-10-05 14:13:14] INFO: Filling index table (1/2)
[flye] 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[flye] [2023-10-05 14:13:25] INFO: Filling index table (2/2)
[flye] 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[flye] [2023-10-05 14:13:47] INFO: Extending reads
[flye] [2023-10-05 14:14:53] INFO: Overlap-based coverage: 37
[flye] [2023-10-05 14:14:53] INFO: Median overlap divergence: 0.0587165
[flye] 0% 90% 100% 
[flye] [2023-10-05 14:15:19] INFO: Assembled 2 disjointigs
[flye] [2023-10-05 14:15:19] INFO: Generating sequence
[flye] 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[flye] [2023-10-05 14:15:24] INFO: Filtering contained disjointigs
[flye] 0% 50% 100% 
[flye] [2023-10-05 14:15:28] INFO: Contained seqs: 0
[flye] [2023-10-05 14:15:28] INFO: >>>STAGE: consensus
[flye] [2023-10-05 14:15:28] INFO: Running Minimap2
[flye] [2023-10-05 14:15:50] INFO: Computing consensus
[flye] [2023-10-05 14:16:40] INFO: Alignment error rate: 0.073354
[flye] [2023-10-05 14:16:54] INFO: >>>STAGE: repeat
[flye] [2023-10-05 14:16:54] INFO: Building and resolving repeat graph
[flye] [2023-10-05 14:16:54] INFO: Parsing disjointigs
[flye] [2023-10-05 14:16:54] INFO: Building repeat graph
[flye] 0% 50% 100% 
[flye] [2023-10-05 14:17:04] INFO: Median overlap divergence: 0.0403617
[flye] [2023-10-05 14:17:05] INFO: Parsing reads
[flye] [2023-10-05 14:17:12] INFO: Aligning reads to the graph
[flye] 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100% 
[flye] [2023-10-05 14:17:30] INFO: Aligned read sequence: 184160513 / 185129557 (0.994766)
[flye] [2023-10-05 14:17:30] INFO: Median overlap divergence: 0.0160677
[flye] [2023-10-05 14:17:30] INFO: Mean edge coverage: 37
[flye] [2023-10-05 14:17:30] INFO: Simplifying the graph
[flye] [2023-10-05 14:17:30] INFO: >>>STAGE: contigger
[flye] [2023-10-05 14:17:30] INFO: Generating contigs
[flye] [2023-10-05 14:17:30] INFO: Reading sequences
[flye] [2023-10-05 14:17:34] INFO: Generated 2 contigs
[flye] [2023-10-05 14:17:34] INFO: Added 0 scaffold connections
[flye] [2023-10-05 14:17:34] INFO: >>>STAGE: finalize
[flye] [2023-10-05 14:17:34] INFO: Assembly statistics:
[flye] 
[flye] 	Total length:	4936081
[flye] 	Fragments:	2
[flye] 	Fragments N50:	4683859
[flye] 	Largest frg:	4683859
[flye] 	Scaffolds:	0
[flye] 	Mean coverage:	36
[flye] 
[flye] [2023-10-05 14:17:34] INFO: Final assembly: /path/to/flye/assembly.fasta

(Randomly picked a pretty bad coverage example, woops, but still works as an example of it looking like a flye log!)

Hopefully that's helpful!
BR,
Ian

[MostafaYA]

@incoherentian Thanks - I have indeed overlooked it!

[MostafaYA]

when --trim is enabled, the porechop progress in the log file makes it a bit difficult to get the relevant information from that log file :(